Maj. Gen. Manan Farahi, head of intelligence for the Afghan Defense Ministry, said Kandahari, an Afghan-American, was in the custody of the National Directorate of Security and was being questioned about his role in the disappearances and deaths of up to 17 people.
Afghan investigators said they had a videotape showing Kandahari torturing Sayid Mohammad, a civilian, and believe they have evidence to prove he was involved in the disappearances of other civilians.
Investigators found the bodies of 10 people near the American Special Forces A Team base in the Nerkh District of Wardak Province after the Americans left in April, The New York Times reported.
An American official said in May the Special Forces team was not responsible for the disappearances and deaths.
"We have done three investigations down there, and all absolve [International Security Assistance Force] forces and Special Forces of all wrongdoing," the official, whose name and affiliation were not reported. "It is simply not true."
Farahi said the abuses continued even after Kandahari fled the base in January when Afghan President Hamid Karzai demanded his arrest.
"Everybody knows and you should know that Zakaria Kandahari and these people with him were there with the Americans and were working for the Americans," Farahi said. "Whether they killed people on their own or were directed by the Americans to kill people, it needs extensive investigation. Now that Mr. Kandahari is in custody most of these things will become clear."